Tag Archives: DOE

News about the Integrated Microbial Genomes (IMG) resource

I’ve got a few news items regarding IMG, or Integrated Microbial Genomes, from the DOE Joint Genome Institute. The first item is that their Sept 2010 release occurred this week. IMG is now on version 3.2, has updated features and a bunch of new/revised genomes. I’ve begun updating our tutorial & will let you know when that is released. It’s not the craziest level of tool changes that I’ve seen from this group, but dang, they SURE don’t rest on their laurels! They are constantly changing and improving their interface and database.

If you are involved in microbial research and haven’t already checked out this powerful resource, I strongly suggest that you do. We’ve been training on this resource since 2006 and really believe in its value, which seems to increase with each of their releases. Mary & Trey presented an IMG workshop at NIH recently and it was surprising how many of their researchers were not aware of IMG. We hear that pretty often and it is too bad, it has so much to offer the microbial community and others as well.

The second item is that IMG has an annotation tool specifically designed for undergraduate education. Iddo Friedberg  describes this as ‘Way cool’ in a recent tweet. The program/interface is named the “Integrated Microbial Genomes Annotation Collaboration Toolkit (IMG-ACT)“, and is somewhat associated with the “Interpret a GEBA Genome for Education” project from JGI. “GEBA” stands for Genomic Encyclopedia of Bacteria and Archaea.  Both efforts are aimed at encouraging undergraduate research in microbial genome annotation, which might lead to the ‘alternative science career’ as a biocurator!

You can read all about the tool in their PLoS Biology article “Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum“, or see a tour of the program/interface here. The tour makes the interface seem a bit clunky to me, but well thought out with lots of solutions to problems/issues often associated with undergraduate classes. The paper really provides a nice overview of the concept, collaborations, and initial outcomes of the 2008-2009 program.

Sign-ups are occurring for the 2011-2012 version of the program. The time frame is as follows:

Timeline to Participate:
1. Apply to be part of the 2011-2012 team by Monday, November 5, 2010 (download the application)
2. After acceptance, attend the workshop at the JGI (January 2011)
3. Implement in 2011-2012 academic year

as can be seen at the bottom of this page.

IMG-ACT Reference:
ResearchBlogging.orgDitty, J., Kvaal, C., Goodner, B., Freyermuth, S., Bailey, C., Britton, R., Gordon, S., Heinhorst, S., Reed, K., Xu, Z., Sanders-Lorenz, E., Axen, S., Kim, E., Johns, M., Scott, K., & Kerfeld, C. (2010). Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum PLoS Biology, 8 (8) DOI: 10.1371/journal.pbio.1000448

Friday SNPpets

Welcome to our Friday feature link dump: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

Tip of the Week: from OSTI to a Plethora of Resources

tip_osti_0211092In today’s tip I want to introduce you to a great launch site – from it you can launch into all sorts of information and resources. The site is homepage for The Office of Scientific and Technical Information (OSTI), which is a U.S. Department of Energy (DOE) program – I heard about it in one of the demo talks at ScienceOnline09. I’m going to hop you through some of the interesting sites that I found, but I’m sure with a bit of browsing time you’ll be able to follow your own yellow brick road to government gold (sponsored resources more than money, that is). Enjoy the tip & let me know what your favorite finds are!